1. Recent studies have documented shifts in habitat associations of single tropical tree species from one life stage to the next. However, the community-level consequences of such shifts have not been investigated, and it is not clear whether they would amplify, neutralize or completely alter habitat structuring during the transitions to the adult community.

2. We compared habitat-driven species assemblages at three life stages (i.e. recruitment, juvenile and reproductive stages) and six censuses for tree and shrub species in a fully censused 50-ha plot of Panamanian lowland forest. Habitat types were determined using multivariate regression trees that group areas with similar species composition (i.e. species assemblages) according to their topographical characteristics.

3. Three topographical variables (a topographical wetness index, slope and elevation) were major determinants of species assemblages. When analysing individuals of all life stages together, we found a distinct and temporally consistent structuring of the plot into four dominant habitat types (low and high plateaus, slope and swamp) which was consistent with previous classifications. Basically, the same habitat structuring emerged for the juvenile communities of individual censuses. However, recruits showed a weak and temporally inconsistent habitat structuring.

4. A notable homogenization in species assemblages occurred during the transition from juvenile to reproductive, through both a reduction in the number of species assemblages (in 3 censuses, one large reproductive assemblage covered 93% of the plot, and in others, an additional slope habitat emerged) and a reduction in the classification error. Overall, habitat structuring became noisier and weaker over the 25 years of the study.

5.Synthesis. Our results suggest that mortality processes during the transition from recruits to juveniles must enhance the signal of habitat structuring. However, during the transition to the reproductive stage, species may have lost the advantage of being in the habitat with which they had become associated, or the quality of habitat changed during their life span because of larger climatic changes. The homogeneous assemblages of the reproductive stage could be interpreted as support for neutral theories, but further research is required to unravel the mechanisms behind these intriguing observations.